GaussFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FILTERING/SMOOTHING/GaussFilterAlgorithm.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <cmath>
 
namespace OpenMS
{
//#define DEBUG_FILTERING
 
  class OPENMS_DLLAPI GaussFilter :
    public ProgressLogger,
    public DefaultParamHandler
  {
public:
    GaussFilter();
 
    ~GaussFilter() override;
 
    void filter(MSSpectrum & spectrum)
    {
      typedef std::vector<double> ContainerT;
 
      // make sure the right data type is set
      spectrum.setType(SpectrumSettings::PROFILE);
      bool found_signal = false;
      const Size data_size = spectrum.size();
      ContainerT mz_in(data_size), int_in(data_size), mz_out(data_size), int_out(data_size);
 
      // copy spectrum to container
      for (Size p = 0; p < spectrum.size(); ++p)
      {
        mz_in[p] = spectrum[p].getMZ();
        int_in[p] = static_cast<double>(spectrum[p].getIntensity());
      }
 
      // apply filter
      ContainerT::iterator mz_out_it = mz_out.begin();
      ContainerT::iterator int_out_it = int_out.begin();
      found_signal = gauss_algo_.filter(mz_in.begin(), mz_in.end(), int_in.begin(), mz_out_it, int_out_it);
 
      // If all intensities are zero in the scan and the scan has a reasonable size, throw an exception.
      // This is the case if the Gaussian filter is smaller than the spacing of raw data
      if (!found_signal && spectrum.size() >= 3)
      {
        String error_message = "Found no signal. The Gaussian width is probably smaller than the spacing in your profile data. Try to use a bigger width.";
        if (spectrum.getRT() > 0.0)
        {
          error_message += String(" The error occurred in the spectrum with retention time ") + spectrum.getRT() + ".";
        }
        OPENMS_LOG_ERROR << error_message << std::endl;
      }
      else
      {
        // copy the new data into the spectrum
        ContainerT::iterator mz_it = mz_out.begin();
        ContainerT::iterator int_it = int_out.begin();
        for (Size p = 0; mz_it != mz_out.end(); mz_it++, int_it++, p++)
        {
          spectrum[p].setIntensity(*int_it);
          spectrum[p].setMZ(*mz_it);
        }
      }
    }
 
    void filter(MSChromatogram & chromatogram)
    {
      typedef std::vector<double> ContainerT;
 
      if (param_.getValue("use_ppm_tolerance").toBool())
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 
          "GaussFilter: Cannot use ppm tolerance on chromatograms");
      }
 
      bool found_signal = false;
      const Size data_size = chromatogram.size();
      ContainerT rt_in(data_size), int_in(data_size), rt_out(data_size), int_out(data_size);
 
      // copy spectrum to container
      for (Size p = 0; p < chromatogram.size(); ++p)
      {
        rt_in[p] = chromatogram[p].getRT();
        int_in[p] = chromatogram[p].getIntensity();
      }
 
      // apply filter
      ContainerT::iterator mz_out_it = rt_out.begin();
      ContainerT::iterator int_out_it = int_out.begin();
      found_signal = gauss_algo_.filter(rt_in.begin(), rt_in.end(), int_in.begin(), mz_out_it, int_out_it);
 
      // If all intensities are zero in the scan and the scan has a reasonable size, throw an exception.
      // This is the case if the Gaussian filter is smaller than the spacing of raw data
      if (!found_signal && chromatogram.size() >= 3)
      {
        String error_message = "Found no signal. The Gaussian width is probably smaller than the spacing in your chromatogram data. Try to use a bigger width.";
        if (chromatogram.getMZ() > 0.0)
        {
          error_message += String(" The error occurred in the chromatogram with m/z time ") + chromatogram.getMZ() + ".";
        }
        OPENMS_LOG_ERROR << error_message << std::endl;
      }
      else
      {
        // copy the new data into the spectrum
        ContainerT::iterator mz_it = rt_out.begin();
        ContainerT::iterator int_it = int_out.begin();
        for (Size p = 0; mz_it != rt_out.end(); mz_it++, int_it++, p++)
        {
          chromatogram[p].setIntensity(*int_it);
          chromatogram[p].setMZ(*mz_it);
        }
      }
    }
 
    void filterExperiment(PeakMap & map)
    {
      Size progress = 0;
      startProgress(0, map.size() + map.getChromatograms().size(), "smoothing data");
      for (Size i = 0; i < map.size(); ++i)
      {
        filter(map[i]);
        setProgress(++progress);
      }
      for (Size i = 0; i < map.getChromatograms().size(); ++i)
      {
        filter(map.getChromatogram(i));
        setProgress(++progress);
      }
      endProgress();
    }
 
protected:
 
    GaussFilterAlgorithm gauss_algo_;
 
    double spacing_;
 
    // Docu in base class
    void updateMembers_() override;
  };
 
} // namespace OpenMS